The pair fled the centre on Sunday night after smashing up a classroom, breaking furniture and computers, and escaping onto the roof and over the barbed wire fence.

Commander Murphy said officers came across the pair on Tuesday in a car in Fannie Bay and pursued them about 15 kilometres back to the juvenile detention centre.

"We had to gauge that (pursuit) very carefully ... the pursuit balanced with the fact they were escaped prisoners, known property offenders and a danger to the public," he told AAP.

The boys rammed the car through Don Dale's roller doors and then lapped the inside perimeter doing burn-outs for almost an hour before surrendering to police.

Investigators are interviewing the pair and preparing to lay charges that are expected to include criminal damage, escaping from lawful custody, unlawful use of a motor vehicle and traffic offences, Commander Murphy said.

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Authorities say Tuesday's incident was not the first ram-raid of Don Dale: three teenaged inmates crashed a trade car into the internal fence in February, and in June last year a group of five rammed the centres's main gates with a stolen ute.

Chief Minister Adam Giles said of Tuesday's ram-raid return: "We're dealing with some people in our community who are so disconnected from society that they think this is OK to do.

"My heart goes out to those youth, but my heart also goes out to the security officers working to protect and detain these youth, and to the wider community who don't want their houses broken into.

"If we need to get tough on these youth who are causing trouble we will do that ... protection of the community is of fundamental importance."